ArticleNature methods2014
Characterizing bacterial gene circuit dynamics with optically programmed gene expression signals.
Article in Nature methods, 2014. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 91 papers.
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Who cites it
91 citing papers in PubMed.
- Closed-Loop Optogenetic Control in a Microplate Reader.ACS synthetic biology · 2026Article
- Dynamic heterogeneity in an E. coli stress response regulon mediates gene activation and antimicrobial peptide tolerance.Cell reports · 2026Article
- A stationary phase-specific bacterial green light sensor for enhancing metabolite production.Nature communications · 2025Article
- A simplified two-plasmid system for orthogonal control of mammalian gene expression using light-activated CRISPR effector.BMC biotechnology · 2025Article
- Developing Quorum Sensing-Based Collaborative Dynamic Control System in Halomonas TD01.Advanced science (Weinheim, Baden-Wurttemberg, Germany) · 2025Article
- Optogenetic Control of B. subtilis Gene Expression Using the CcaSR System.Methods in molecular biology (Clifton, N.J.) · 2025Article
- Light-dependent modulation of protein localization and function in living bacteria cells.Nature communications · 2024Article
- The need for adaptability in detection, characterization, and attribution of biosecurity threats.Nature communications · 2024Review
- Article
- Macrophages and the microbiome in chronic obstructive pulmonary disease.European respiratory review : an official journal of the European Respiratory Society · 2024Review
- Light Control in Microbial Systems.International journal of molecular sciences · 2024Review
- Deep model predictive control of gene expression in thousands of single cells.Nature communications · 2024Article
- Light-inducible protein degradation ineLife · 2024Article
- Dynamic Gene Expression Mitigates Mutational Escape in Lysis-Driven Bacteria Cancer Therapy.Biodesign research · 2024Article
- Accelerating Genetic Sensor Development, Scale-up, and Deployment Using Synthetic Biology.Biodesign research · 2024Article
- Algorithmic Programming of Sequential Logic and Genetic Circuits for Recording Biochemical Concentration in a Probiotic Bacterium.ACS synthetic biology · 2023Article
- From qualitative to quantitative: the state of the art and challenges for plant synthetic biology.Quantitative biology (Beijing, China) · 2023Review
- Deep Neural Networks for Predicting Single-Cell Responses and Probability Landscapes.ACS synthetic biology · 2023Article
- Conformational-switch biosensors as novel tools to support continuous, real-time molecular monitoring in lab-on-a-chip devices.Lab on a chip · 2023Review
- Optogenetic control of beta-carotene bioproduction in yeast across multiple lab-scales.Frontiers in bioengineering and biotechnology · 2023Article
31 more citing papers are in PubMed but not listed here.
Corrections and comments
PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.
Authors and funding
5 authors.
Funding
No grant is acknowledged in the PubMed record.
Abstract
Gene circuits are dynamical systems that regulate cellular behaviors, often using protein signals as inputs and outputs. Here we have developed an optogenetic 'function generator' method for programming tailor-made gene expression signals in live bacterial cells. We designed precomputed light sequences based on experimentally calibrated mathematical models of light-switchable two-component systems and used them to drive intracellular protein levels to match user-defined reference time courses. We used this approach to generate accelerated and linearized dynamics, sinusoidal oscillations with desired amplitudes and periods, and a complex waveform, all with unprecedented accuracy and precision. We also combined the function generator with a dual fluorescent protein reporter system, analogous to a dual-channel oscilloscope, to reveal that a synthetic repressible promoter linearly transforms repressor signals with an approximate 7-min delay. Our approach will enable a new generation of dynamical analyses of synthetic and natural gene circuits, providing an essential step toward the predictive design and rigorous understanding of biological systems.
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Registered trials
Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.